Hi Alex
when you say it is in the native anatomical space can you elaborate? How
did you create the mask?
Bruce
On Fri, 17 Aug 2012, Alex Kell wrote:
hi freesurfers,
i'm trying to move a volume from a subject's native anatomical space
to that subject's surface space, and i'm running into
hi bruce,
the mask was generated by morphing a binary mask from CVS space back to the
subject's anatomical space. the cvs mask was generated from a functional
parcellation algorithm our lab uses.
if it's useful -- the registration header in the anatomical-space mask is
identical to the
does it align with say the orig.mgz when viewed in tkmedit?
On Fri, 17 Aug
2012, Alex Kell wrote:
hi bruce,
the mask was generated by morphing a binary mask from CVS space back to the
subject's anatomical space. the cvs mask was generated from a functional
parcellation algorithm our lab
Hi Alex
I think Doug is the one to help you. Hopefully he has enough info at this
point
Bruce
On Fri, 17 Aug 2012, Alex Kell wrote:
i don't really use tkmedit. with freeview it's right where it should be --
e.g., see attached.
alex
On Fri, Aug 17, 2012 at 11:43 AM, Bruce Fischl
Hi Alex, does the output of mri_vol2surf look ok on the surface? When
you run mri_cor2label, you should use the white or pial surface instead
of inflated, but I don't think that is the problem here. Another thing
to look at is
tkregister2 --mov volumetric-mask --regheader --reg junk.dat --s
hi doug,
i can't visualize it. when i try to use tksurfer (or even mris_info) i get
the following error messages repeatedly (like 100 times and keeps going
until i interrupt the call).
freadFloat: fread failed
No such file or directory
i tried mri_vol2surf using the white surface instead of
what is your command line? You have to load it as an overlay, it isn't a
surface just a scalar field over the surface
On Fri, 17 Aug 2012, Alex Kell
wrote:
hi doug,
i can't visualize it. when i try to use tksurfer (or even mris_info) i get
the following error messages repeatedly (like 100
Ah, I did not see that you had used inflated in your original vol2surf
command. That is definitely the source of the misplaced label. The
surf_name.mgz file is not a surface, it is an overlay. If you are trying
to load it as a surface in tksurfer (or getting info from mris_info),
then it will
ah, thanks -- i didn't realize the distinction.
also, i think i've figured out what was wrong. i shouldn't sample to the
inflated surface -- i should sample to the white surface.
the call that lead to misplacement:
mri_vol2surf --mov volumetric_mask --regheader subj_id --hemi rh
--inflated --o
Sure, glad it worked out
Bruce
On Aug 17, 2012, at 3:03 PM, Alex Kell alexk...@mit.edu wrote:
ah, thanks -- i didn't realize the distinction.
also, i think i've figured out what was wrong. i shouldn't sample to the
inflated surface -- i should sample to the white surface.
the call
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